1dxf

From Proteopedia

(Difference between revisions)

Revision as of 09:32, 21 July 2021

2-dehydro-3-deoxy-galactarate aldolase from Escherichia coli in complex with pyruvate

Structural highlights

1dxf is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
NonStd Res:
Related:	1dxe
Activity:	2-dehydro-3-deoxyglucarate aldolase, with EC number 4.1.2.20
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[GARL_ECOLI] Catalyzes the reversible retro-aldol cleavage of both 5-keto-4-deoxy-D-glucarate and 2-keto-3-deoxy-D-glucarate to pyruvate and tartronic semialdehyde.^[1] [REFERENCE:5]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Carbon-carbon bond formation is an essential reaction in organic chemistry and the use of aldolase enzymes for the stereochemical control of such reactions is an attractive alternative to conventional chemical methods. Here we describe the crystal structures of a novel class II enzyme, 2-dehydro-3-deoxy-galactarate (DDG) aldolase from Escherichia coli, in the presence and absence of substrate. The crystal structure was determined by locating only four Se sites to obtain phases for 506 protein residues. The protomer displays a modified (alpha/beta)(8) barrel fold, in which the eighth alpha-helix points away from the beta-barrel instead of packing against it. Analysis of the DDG aldolase crystal structures suggests a novel aldolase mechanism in which a phosphate anion accepts the proton from the methyl group of pyruvate.

Crystal structures of the metal-dependent 2-dehydro-3-deoxy-galactarate aldolase suggest a novel reaction mechanism.,Izard T, Blackwell NC EMBO J. 2000 Aug 1;19(15):3849-56. PMID:10921867^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Hubbard BK, Koch M, Palmer DR, Babbitt PC, Gerlt JA. Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli. Biochemistry. 1998 Oct 13;37(41):14369-75. PMID:9772162 doi:http://dx.doi.org/10.1021/bi981124f
↑ Izard T, Blackwell NC. Crystal structures of the metal-dependent 2-dehydro-3-deoxy-galactarate aldolase suggest a novel reaction mechanism. EMBO J. 2000 Aug 1;19(15):3849-56. PMID:10921867 doi:10.1093/emboj/19.15.3849

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1dxf"

@@ Line 3: / Line 3: @@
 <StructureSection load='1dxf' size='340' side='right'caption='[[1dxf]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1dxf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DXF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DXF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1dxf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DXF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DXF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dxe|1dxe]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dxe|1dxe]]</div></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-dehydro-3-deoxyglucarate_aldolase 2-dehydro-3-deoxyglucarate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.20 4.1.2.20] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2-dehydro-3-deoxyglucarate_aldolase 2-dehydro-3-deoxyglucarate aldolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.20 4.1.2.20] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dxf OCA], [http://pdbe.org/1dxf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dxf RCSB], [http://www.ebi.ac.uk/pdbsum/1dxf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dxf ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dxf OCA], [https://pdbe.org/1dxf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dxf RCSB], [https://www.ebi.ac.uk/pdbsum/1dxf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dxf ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GARL_ECOLI GARL_ECOLI]] Catalyzes the reversible retro-aldol cleavage of both 5-keto-4-deoxy-D-glucarate and 2-keto-3-deoxy-D-glucarate to pyruvate and tartronic semialdehyde.<ref>PMID:9772162</ref> [REFERENCE:5]
+[[https://www.uniprot.org/uniprot/GARL_ECOLI GARL_ECOLI]] Catalyzes the reversible retro-aldol cleavage of both 5-keto-4-deoxy-D-glucarate and 2-keto-3-deoxy-D-glucarate to pyruvate and tartronic semialdehyde.<ref>PMID:9772162</ref> [REFERENCE:5]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]

1dxf

From Proteopedia

Revision as of 09:32, 21 July 2021

2-dehydro-3-deoxy-galactarate aldolase from Escherichia coli in complex with pyruvate

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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